Metadata-Version: 2.1
Name: modelestimator-v2
Version: 2.1.3
Summary: Program for estimating amino acid replacement rates
Home-page: https://github.com/arvestad/modelestimator-v2
Author: Ruben Ridderström and Lars Arvestad
Author-email: ruben.ridderstrom@gmail.com
License: GPLv3
Description: # modelestimator --- Infer sequence evolution rate matrices from a MSA
        
        
        ## Example usage
        
        ``` shell
            modelestimator -t 0.001 file1.fa file2.fa file3.fa
        ```
        Infer a rate matrix (written to stdout) from three alignment files in Fasta format.
        The output is PAML format by default, and therefore applicable in a number of
        available phylogenetic softwares.
        
        ``` shell
            modelestimator -b 200 file.fa
        ```
        Try the experimental bootstrapping feature (200 replicates) on a Fasta multialignment.
        
        ## Syntax
        
        ```
        modelestimator <options> infiles
        ```
        
        
        `<format>` should be either FASTA, STOCKHOLM or PHYLIP format.
        
        Output is a rate matrix and residue distribution vector.
        
        ### Options
        
        ```
          -h, --help            show this help message and exit
          --version             show program's version number and exit
          -a {iqtree,matlab,mrbayes,octave,paml,phyml}, --application {iqtree,matlab,mrbayes,octave,paml,phyml}
                                Choose output format to suit the application you want
                                to use for inference. The 'iqtree', 'paml' and 'phyml'
                                options are identical. The 'matlab' and 'octave'
                                optins are for import into MatLab-compatible programs
                                and are presenting the actual Q matrix rather than the
                                R matrix used by PAML/PhyML, etc. Default: paml
          -f {fasta,clustal,nexus,phylip,stockholm}, --format {fasta,clustal,nexus,phylip,stockholm}
                                Specify sequence format of input files. Default: fasta
          -t T, --threshold T   Stop when consecutive iterations do not change by more
                                than T. Default: 0.001
          -b N, --bootstrap N   Estimate the rate matrix using bootstrapping by
                                computing N resampled replicates of the input
                                multialignment. For each replicate, a rate matrix is
                                computed. The mean matrix the elementwise standard
                                deviation is returned. Only one infile should be given
                                in this mode.
          -B N, --bootstrapped_quality N
                                Estimate the quality of the rate matrix estimate using
                                a bootstrap procedure. The multialignment is resampled
                                N times and a Q matrix is computed for each replicate.
                                Then the difference (matrix norm) between rate matrix
                                estimated without resampling and each bootstrapped Q
                                is computed and the mean difference is returned. Only
                                one infile should be given in this mode. Returns
                                bootstrap norm.
        ```
        
Platform: UNKNOWN
Description-Content-Type: text/markdown; charset=UTF-8
